Genomic variants reveal differential evolutionary constraints on human transglutaminases and point towards unrecognized significance of transglutaminase 2

Abstract

Transglutaminases (TGMs) catalyze Ca2+-dependent transamidation of proteins with specified roles in blood clotting (F13a) and in cornification (TGM1, TGM3). The ubiquitous TGM2 has well described enzymatic and non-enzymatic functions but in-spite of numerous studies its physiological function in humans has not been defined. We compared data on non-synonymous single nucleotide variations (nsSNVs) and loss-of-function variants on TGM1-7 and F13a from the Exome aggregation consortium dataset, and used computational and biochemical analysis to reveal the roles of damaging nsSNVs of TGM2. TGM2 and F13a display rarer damaging nsSNV sites than other TGMs and sequence of TGM2, F13a and TGM1 are evolutionary constrained. TGM2 nsSNVs are predicted to destabilize protein structure, influence Ca2+ and GTP regulation, and non-enzymatic interactions, but none coincide with conserved functional sites. We have experimentally characterized six TGM2 allelic variants detected so far in homozygous form, out of which only one, p.Arg222Gln, has decreased activities. Published exome sequencing data from various populations have not uncovered individuals with homozygous loss-of-function variants for TGM2, TGM3 and TGM7. Thus it can be concluded that human transglutaminases differ in harboring damaging variants and TGM2 is under purifying selection suggesting that it may have so far not revealed physiological functions.

Spotlight on the transglutaminase 2 gene: a focus on genomic and transcriptional aspects

“…that regulation and modulation of TGM2 expression could affect heavily these pathways, thanks to its relationships with the signalling of NF-κB, RA, IL-6, TGF-β, HRE, Ap1 and GRE. In this context, it would be relevant to investigate effects of SNPs at transcription factor-binding sites to improve molecular knowledge of DNA/ protein interactions, even more so after the studies carried out on SNPs in exonic sequences which bring about no relevant modifications of enzyme functions [18,37,44]. Actually, very few SNPs are associated with pathological phenotypes [43,45,50,51].…”

“…Only a few (29/272) non-synonymous single-nucleotide variants (nsSNV) in TGM2 gene [44] can produce loss of function, when analyzed using the database ExAC (Exome Aggregation Consortium browser) and the scores Sorting Intolerant From Tolerant (SIFT) and Polymorphism Phenotyping (PolyPhen). The authors investigated both the effects of the rare SNVs on the conserved sites involved in important functional roles and the sites or motifs interested with protein-protein interactions focusing the attention on homozygotes-related nsSNVs.…”

“…Six variants with an allele frequency of <0.5% (R76H; R222Q; R433Q; V542F; P612T; D671N) were (A) Stars represent natural variants of the protein linked to SNP and described in the Uniprot database, where white stars indicate natural variants associated with the mutations I331N and G660V reported in the literature [42,43], while other stained stars have the same colour code as reported below. The variants identified by black arrows have been cloned and tested by Király et al [18], who reported for some of them (underlined) loss of transglutaminase activity in the enzyme bound to FN, whereas that by blue arrow is associated with phenotype with the evidence of functional modification [44]. The white rhombus represents mutation N333S in a subject with MODY [43,45].…”

“…The relative low number of SNPs in the coding region of this protein suggests an evolutionary strong selection on the structure needed to conserve its functional features [18,44,51]. As a consequence, it could be possible that a lot of missense mutations would not be selected during evolution and finally from the feasible genotypes in the population.…”

Biochemical characterisation of human transglutaminase 4

“…hTG4 is an autoantigen in autoimmune polyendocrine syndrome type 1, and contributes to the development of prostatitis resulting in male infertility [21]. These presumed roles of hTG4 look controversial since evolutional biology studies claim that the gene of TG4 (TGM4) is dead, has lost its biological function due to the lack of copulatory plug formation [22] and its high polymorphism in humans [23] indicates low evolutional pressure and dispensability. Indeed, there is a lack of both detailed biochemical characterisation and demonstration of the biological significance of hTG4 in physiological and pathological processes.…”